Background: Over the past decade, substantial global investment has been made to support health systems and policy research (HSPR), with considerable resources allocated to training. In Canada, signs point to a larger and more highly skilled HSPR workforce, but little is known about whether growth in HSPR human resource capacity is aligned with investments in other research infrastructure, or what happens to HSPR graduates following training. Methods: We collected data from the Canadian Institutes of Health Research, Canada’s national health research funding agency, and the Canadian Association for Health Services and Policy Research on recent graduates in the HSPR workforce. We also surveyed 45 Canadian HSPR training programs to determine what information they collect on the career experiences of graduates. Results: No university programs are currently engaged in systematic follow-up. Collaborative training programs funded by the national health research funding agency report performing short-term mandated tracking activities, but whether and how data are used is unclear. No programs collected information about whether graduates were using skills obtained in training, though information collected by the national funding agency suggests a minority (<30%) of doctoral-level trainees moving on to academic careers. Conclusions: Significant investments have been made to increase HSPR capacity in Canada and around the world but no systematic attempts to evaluate the impact of these investments have been made. As a research community, we have the expertise and responsibility to evaluate our health research human resources and should strive to build a stronger knowledge base to inform future investment in HSPR research capacity.